JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / gui / ChimeraViewFrame.java

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 09451dc..c30a418 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -249,6 +249,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqs)
   {
     createProgressBar();
+    // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
     String[][] chains = extractChains(seqs);
     jmb = new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
@@ -270,6 +271,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
       {
         closeViewer(false);
@@ -302,6 +304,9 @@ public class ChimeraViewFrame extends StructureViewerBase
                   .getAllPDBEntries();
           if (pdbrefs != null && pdbrefs.size() > 0)
           {
+            // FIXME: SequenceI.PDBEntry[0] chain mapping used for
+            // ChimeraViewFrame. Is this even used ???
+
             chain = pdbrefs.get(0).getChainCode();
           }
         }
@@ -460,6 +465,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             MessageManager.getString("label.all"));
     menuItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         allChainsSelected = true;
@@ -482,6 +488,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       menuItem = new JCheckBoxMenuItem(chainName, true);
       menuItem.addItemListener(new ItemListener()
       {
+        @Override
         public void itemStateChanged(ItemEvent evt)
         {
           if (!allChainsSelected)
@@ -523,6 +530,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param closeChimera
    *          if true, close any linked Chimera process; if false, prompt first
    */
+  @Override
   public void closeViewer(boolean closeChimera)
   {
     if (jmb != null && jmb.isChimeraRunning())
@@ -553,6 +561,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * Open any newly added PDB structures in Chimera, having first fetched data
    * from PDB (if not already saved).
    */
+  @Override
   public void run()
   {
     _started = true;
@@ -651,7 +660,8 @@ public class ChimeraViewFrame extends StructureViewerBase
           {
             int pos = filePDBpos.get(num).intValue();
             long startTime = startProgressBar("Chimera "
-                    + MessageManager.getString("status.opening_file"));
+                    + MessageManager.getString("status.opening_file_for")
+                    + " " + pe.getId());
             jmb.openFile(pe);
             jmb.addSequence(pos, jmb.getSequence()[pos]);
             File fl = new File(pe.getFile());
@@ -699,6 +709,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       {
         new Thread(new Runnable()
         {
+          @Override
           public void run()
           {
             alignStructs_withAllAlignPanels();
@@ -722,6 +733,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
+    // FIXME: this is duplicated code with Jmol frame ?
     String filePath = null;
     Pdb pdbclient = new Pdb();
     AlignmentI pdbseq = null;
@@ -1091,6 +1103,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     }
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI ucs)
   {
     jmb.setJalviewColourScheme(ucs);